Volume 24, Issue 8, Pages 2179-2190.e7 (August 2018) Diversity of Interneurons in the Dorsal Striatum Revealed by Single-Cell RNA Sequencing and PatchSeq  Ana B. Muñoz-Manchado, Carolina Bengtsson Gonzales, Amit Zeisel, Hermany Munguba, Bo Bekkouche, Nathan G. Skene, Peter Lönnerberg, Jesper Ryge, Kenneth D. Harris, Sten Linnarsson, Jens Hjerling-Leffler  Cell Reports  Volume 24, Issue 8, Pages 2179-2190.e7 (August 2018) DOI: 10.1016/j.celrep.2018.07.053 Copyright © 2018 The Author(s) Terms and Conditions

Cell Reports 2018 24, 2179-2190.e7DOI: (10.1016/j.celrep.2018.07.053) Copyright © 2018 The Author(s) Terms and Conditions

Figure 1 Single-Cell Sequencing Approaches in the Mouse Dorsal Striatum (A) Left: schematic representation of the experimental workflow (dataset A). Right: hierarchical analysis of neuronal clusters from dataset A. Below: heatmap showing the expression of the 131 most informative genes after BackSPIN analysis. (B) tSNE analysis of dataset A. (C) Left: schematic representation of the experimental workflow (dataset B). Right: hierarchical analysis of clusters obtained from dataset B. Below: heatmap showing the expression of the 270 most informative genes after BackSPIN analysis. (D) tSNE analysis of dataset B. (E) Predictive power of cluster identities using a trained random forest classifier on dataset B. See also Figure S1. Cell Reports 2018 24, 2179-2190.e7DOI: (10.1016/j.celrep.2018.07.053) Copyright © 2018 The Author(s) Terms and Conditions

Figure 2 Characterization and Validation of the Striatal Interneuron Populations Obtained after Single-Cell Sequencing (A) Expression of main markers (molecular counts per individual cell) in dataset A. (B) Left: in situ hybridizations showing the co-expression of Pthlh, Pvalb, Trh, Th, Chodl, and Sst in the indicated combinations. Arrowheads show co-expression of Pthlh and Pvalb, Th and Trh, or Chodl and Sst. The arrow represents Pthlh-positive, Pvalb-negative cells, and stars represent Trh-positive cells and Th-positive, Trh-negative cells. Right: quantifications with the number of mice indicated in brackets (C) Expression of main markers (molecular counts per individual cell) in dataset B. (D) Representative in situ hybridization showing the co-expression of Sst, Tac1, Chodl, Mia, Npy, and Cck in the indicated combinations. Arrowheads indicate co-expression of either Sst, Tac1, and Chodl or Npy and Mia. Stars represent Sst-positive cells co-expressing either Chodl or Npy. Error bars represent mean ± SEM. See also Figure S2. Cell Reports 2018 24, 2179-2190.e7DOI: (10.1016/j.celrep.2018.07.053) Copyright © 2018 The Author(s) Terms and Conditions

Figure 3 Latent Factor Correlates with Gradient-Wise Gene Expression Changes within Pthlh, Sst, and Th Populations (A) Left: tSNE of Pthlh population with the distribution of the latent factor or the expression of Pvalb. Right: scatterplot showing correlation of latent factor and Pvalb expression and the quantification of the in situ hybridization (dots/cell), correlating Pthlh and Pvalb (3 mice, 257 cells). (B) Left: tSNE of Sst population with the distribution of the latent factor or the expression of Tac1. Right: scatterplot showing correlation of latent factor and Tac1 expression and the quantification of the in situ hybridization (dots/cell), correlating Chodl and Tac1 within Sst+ cells (3 mice, 206 cells). (C) Left: tSNE of Th population with the distribution of the latent factor or the expression of Trh. Right: scatterplot showing correlation of latent factor and Trh expression and the quantification of the in situ hybridization (dots/cell), correlating Trh and Th (4 mice, 207 cells). Analyses were done on dataset B. r and p values were acquired using Pearson’s correlation. See also Table S1. Cell Reports 2018 24, 2179-2190.e7DOI: (10.1016/j.celrep.2018.07.053) Copyright © 2018 The Author(s) Terms and Conditions

Figure 4 The Pthlh Population: Pvalb Co-expressing Cells and Spatial Organization (A) Molecular counts of Pthlh and Pvalb in each cell from BackSPIN analysis in both datasets, along with Pvalb expression labeled in red on tSNE plots. (B) Representative in situ hybridization showing the distribution in the dorsoventral and mediolateral axis of Pthlh and Pvalb expression. (C) Correlation of Pthlh and Pvalb expression with mediolateral or dorsoventral axis cell position. r and p values were acquired using Pearson’s correlation. (D) Volcano plot of genes with anti-correlation (blue) or correlation (red) to Pvalb. The y axis represents the log10 adjusted p value, and the x axis shows the rho value, both acquired using Spearman’s rank correlation coefficient. See also Figure S3 and Table S2. Cell Reports 2018 24, 2179-2190.e7DOI: (10.1016/j.celrep.2018.07.053) Copyright © 2018 The Author(s) Terms and Conditions

Figure 5 Electrophysiological Properties within the Pthlh Population Revealed Using PatchSeq (A) Schematic of the PatchSeq protocol. (B) Representative traces of electrophysiological subtypes detected in the mouse lines used for the recordings. (C) Principal-component analysis (PCA) based on 19 electrophysiological parameters from 98 interneurons. The color of the dots refers to the molecular identity acquired by mapping them onto BackSPIN clustering of dataset B. (D) Vector factor map analysis showing how (arrow size) the parameters contribute to (A). (E) Correlations of AP half-width and maximum frequency with normalized Pvalb expression within the Pthlh population. (F) Correlations of AP half-width and maximum frequency with the Pthlh cell latent factor. See also Figures S4 and S5 and Table S3. Cell Reports 2018 24, 2179-2190.e7DOI: (10.1016/j.celrep.2018.07.053) Copyright © 2018 The Author(s) Terms and Conditions

Figure 6 Comparing Single-Cell Transcriptomes of Interneurons from the Striatum and Cortex and Hippocampus (A) tSNE visualizations of the individual transcriptome of striatal (dataset A) and cortical-hippocampal interneurons. (B) Hierarchical clustering of the same cell populations shown in (A). (C) Differential gene expression analysis of striatal Pvalb-positive cells and their cortical counterparts. The y axis represents the log10 (p value) acquired using Wilcoxon rank-sum test, and the x axis shows the log2 (fold change). Significantly differentially expressed genes are marked in red. (D) tSNE plots showing examples of differentially expressed genes in Pvalb+ cells in striatum and cortex and hippocampus. See also Table S4. Cell Reports 2018 24, 2179-2190.e7DOI: (10.1016/j.celrep.2018.07.053) Copyright © 2018 The Author(s) Terms and Conditions

Figure 7 Pvalb-Expressing Interneurons from Striatum and Cortex Exhibit Distinct Intrinsic Properties that Match with Gene Expression (A) PCA using 19 electrophysiological parameters acquired from recordings of 135 cortical and striatal interneurons using Pvalbcre and 5HT3aEGFP mouse lines. (B) Vector factor map analysis showing the parameters used in the PCA in (A) and their contribution (arrow size). (C) PCA based on 15 electrophysiological parameters obtained from Pvalbcre+ cells recorded in layer 5 S1 cortex and dorsolateral striatum. Representative traces are shown in each quarter. (D) Vector factor map analysis showing the parameters used for the PCA in (A) and their contribution (arrow size). (E) Selected parameters that were significantly different between cortical (20) and striatal (25) Pvalbcre+ cells, tested using unpaired t test Benjamini-Hochberg correction for multiple testing (Table S5). Error bars represent mean ± SEM. (F) Expression of selected differentially expressed ion channels involved in fast-spiking behavior in Pvalbcre+ cells. Differential expression was tested upon log transforming the data, using unpaired t test with Benjamini-Hochberg multiple testing correction (Figure S6). FS, fast spiking; FS-like, fast spiking like; IB, intrinsic bursting; LS, late spiking; BiaRS, biphasic AHP regular spiking. See also Figures S6 and S7 and Table S5. Cell Reports 2018 24, 2179-2190.e7DOI: (10.1016/j.celrep.2018.07.053) Copyright © 2018 The Author(s) Terms and Conditions